Command line options:
input.infile.phy_ - The main input file, relaxed phylip format, containing sequence(s) .
input.starting_tree_ - Specify a Newick Starting Tree (-tree)
input.constraint_tree_ - Specify a fixed topology (in the selected file)(-T)
input.custom_exch_file_ - Select the Custom Exchangabilities File; when exchange_rates_ = -rr
input.custom_profile_ - Select the Profile of Equilibrium Frequencies File; when profile_mixture eq "custom"
User Configurable Parameters.
vparam.runtime_ - (Float) Maximum Hours to Run (up to 168 hours)
vparam.num_sites_ - (Integer) Number of sites in the data set no default; required
vparam.datatype_ - (Switch)My data set contains amino acids; (dna, protein, unk), no default; required.
Convergence Parameters
vparam.set_seed_ - (Integer) Enter seed value (no default)
vparam.checkinterval_ - (Integer) Number of seconds to wait between checks for convergence. default=600.
vparam.burninval_ - (Integer) Number of cycles to exclude from convergence checks. default=500
vparam.acceptdiffval_ - (Float) Maximum \maxdiff" value to accept. default=0.1.
vparam.acceptsizeval_ - (Integer) Minimum Effective Size. default=50
vparam.giveupval_ - (Integer) Minimum number of cycles before giving up if "maxdiff" is still 1 (Analysis is stuck). Default=10000
vparam.constant_sitesr_ - (Swtich) Remove Constant Sites (-dc) default=1
vparam.saving_freq_ - (Integer) Save every (-x); default=1
vparam.stop_at_ - (Integer) Number of points after which the chain should stop (-1 = forever); default=-1
vparam.save_detmodelconf_ - (Switch) Save detailed model configuration for each point(-s)
Evolutionary Models
vparam.num_gammacats_ - (Integer) Number of Categories for the discrete gamma distribution (-dgam)
vparam.exchange_rates_ - (Excl) Exchange Rates -gtr, -poisson,-lg, -wag,-jtt,-mtrev,-mtzoa,-mtart,-rr; default=-poisson
vparam.profile_mixture_ - (Excl) Profile Mixture: dp; ncatn, catfic, custom; default=dp
vparam.categories_ - (Integer) Number of Fixed Components (-ncat N); when profile_mixture_ eq "ncatn"
vparam.predefined_profiles_ - (Excl) Choose a Predefined Profile; when profile_mixture_ eq "catfix"; WLSR5,C20,C30,C40,C50,C60 (no default)
vparam.mutsel_model_ - (Switch) Use Codon Alignments Only; default = 0
vparam.mtvert_codons_ (Switch) Use Vertebrate Mitochondrial Genetic Code; default=0
